Abstract

The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible polymer chains in the presence of different degrees of crowding. From the analysis of the looping–unlooping rates and the looping probabilities of the chain ends we show that the presence of small crowders typically slows down the chain dynamics but larger crowders may in fact facilitate the looping. We rationalise these non-trivial and often counterintuitive effects of the crowder size on the looping kinetics in terms of an effective solution viscosity and standard excluded volume. It is shown that for small crowders the effect of an increased viscosity dominates, while for big crowders we argue that confinement effects (caging) prevail. The tradeoff between both trends can thus result in the impediment or facilitation of polymer looping, depending on the crowder size. We also examine how the crowding volume fraction, chain length, and the attraction strength of the contact groups of the polymer chain affect the looping kinetics and hairpin formation dynamics. Our results are relevant for DNA looping in the absence and presence of protein mediation, DNA hairpin formation, RNA folding, and the folding of polypeptide chains under biologically relevant high-crowding conditions.

For reproduction of material from NJC:
[Original citation] - Published by The Royal Society of Chemistry (RSC) on behalf of the
Centre National de la Recherche Scientifique (CNRS) and the RSC.

For reproduction of material from PCCP:
[Original citation] - Published by the PCCP Owner Societies.

For reproduction of material from PPS:
[Original citation] - Published by The Royal Society of Chemistry (RSC) on behalf of the
European Society for Photobiology, the European Photochemistry Association, and
RSC.

For reproduction of material from all other RSC journals:
[Original citation] - Published by The Royal Society of Chemistry.

Information about reproducing material from RSC articles with different licences
is available on our Permission Requests page.